/*
* The MIT License
*
* Copyright (c) 2014 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.illumina;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.programgroups.Illumina;
import picard.cmdline.Option;
import picard.cmdline.StandardOptionDefinitions;
import picard.illumina.parser.ReadStructure;
import picard.illumina.parser.Tile;
import picard.illumina.parser.TileMetricsUtil;
import htsjdk.samtools.metrics.MetricBase;
import htsjdk.samtools.metrics.MetricsFile;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.samtools.util.Log;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Collection;
import java.util.Map;
/**
* Command-line wrapper around {@link IlluminaLaneMetricsCollector}.
* @author mccowan
*/
@CommandLineProgramProperties(
usage = CollectIlluminaLaneMetrics.USAGE,
usageShort = CollectIlluminaLaneMetrics.USAGE,
programGroup = Illumina.class
)
public class CollectIlluminaLaneMetrics extends CommandLineProgram {
static final String USAGE = "Collects Illumina lane metrics for the given basecalling analysis directory";
@Option(doc = "The Illumina run directory of the run for which the lane metrics are to be generated")
public File RUN_DIRECTORY;
@Option(doc = "The directory to which the output file will be written")
public File OUTPUT_DIRECTORY;
@Option(doc = "The prefix to be prepended to the file name of the output file; an appropriate suffix will be applied", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME)
public String OUTPUT_PREFIX;
@Option(doc= ReadStructure.PARAMETER_DOC, shortName="RS")
public ReadStructure READ_STRUCTURE;
@Override
protected int doWork() {
final MetricsFile<MetricBase, Comparable<?>> laneMetricsFile = this.getMetricsFile();
final MetricsFile<MetricBase, Comparable<?>> phasingMetricsFile = this.getMetricsFile();
IlluminaLaneMetricsCollector.collectLaneMetrics(RUN_DIRECTORY, OUTPUT_DIRECTORY, OUTPUT_PREFIX, laneMetricsFile, phasingMetricsFile, READ_STRUCTURE);
return 0;
}
public static void main(final String[] args) {
new CollectIlluminaLaneMetrics().instanceMainWithExit(args);
}
/**
* Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
*/
public static class IlluminaLaneMetricsCollector {
private final static Log LOG = Log.getInstance(IlluminaLaneMetricsCollector.class);
/** Returns a partitioned collection of lane number to Tile objects from the provided basecall directory. */
public static Map<Integer, Collection<Tile>> readLaneTiles(final File illuminaRunDirectory, final ReadStructure readStructure) {
final Collection<Tile> tiles;
try {
tiles = TileMetricsUtil.parseTileMetrics(TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(illuminaRunDirectory), readStructure);
} catch (final FileNotFoundException e) {
throw new PicardException("Unable to open laneMetrics file.", e);
}
return CollectionUtil.partition(tiles,
new CollectionUtil.Partitioner<Tile, Integer>() {
@Override
public Integer getPartition(final Tile tile) {
return tile.getLaneNumber();
}
});
}
/** Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files */
public static void collectLaneMetrics(final File runDirectory, final File outputDirectory, final String outputPrefix,
final MetricsFile<MetricBase, Comparable<?>> laneMetricsFile,
final MetricsFile<MetricBase, Comparable<?>> phasingMetricsFile,
final ReadStructure readStructure) {
final Map<Integer, Collection<Tile>> laneTiles = readLaneTiles(runDirectory, readStructure);
writeLaneMetrics(laneTiles, outputDirectory, outputPrefix, laneMetricsFile);
writePhasingMetrics(laneTiles, outputDirectory, outputPrefix, phasingMetricsFile);
}
public static File writePhasingMetrics(final Map<Integer, Collection<Tile>> laneTiles, final File outputDirectory,
final String outputPrefix, final MetricsFile<MetricBase, Comparable<?>> phasingMetricsFile) {
for (final Map.Entry<Integer, Collection<Tile>> entry : laneTiles.entrySet()) {
for (final IlluminaPhasingMetrics phasingMetric : IlluminaPhasingMetrics.getPhasingMetricsForTiles(entry.getKey()
.longValue(),
entry.getValue())) {
phasingMetricsFile.addMetric(phasingMetric);
}
}
return writeMetrics(phasingMetricsFile, outputDirectory, outputPrefix, IlluminaPhasingMetrics.getExtension());
}
public static File writeLaneMetrics(final Map<Integer, Collection<Tile>> laneTiles, final File outputDirectory,
final String outputPrefix, final MetricsFile<MetricBase, Comparable<?>> laneMetricsFile) {
for (final Map.Entry<Integer, Collection<Tile>> entry : laneTiles.entrySet()) {
final IlluminaLaneMetrics laneMetric = new IlluminaLaneMetrics();
laneMetric.LANE = entry.getKey().longValue();
laneMetric.CLUSTER_DENSITY = calculateLaneDensityFromTiles(entry.getValue());
laneMetricsFile.addMetric(laneMetric);
}
return writeMetrics(laneMetricsFile, outputDirectory, outputPrefix, IlluminaLaneMetrics.getExtension());
}
private static File writeMetrics(final MetricsFile<MetricBase, Comparable<?>> metricsFile, final File outputDirectory,
final String outputPrefix, final String outputExtension) {
final File outputFile = new File(outputDirectory, String.format("%s.%s", outputPrefix, outputExtension));
LOG.info(String.format("Writing %s lane metrics to %s ...", metricsFile.getMetrics().size(), outputFile));
metricsFile.write(outputFile);
return outputFile;
}
private static double calculateLaneDensityFromTiles(final Collection<Tile> tiles) {
double area = 0;
double clusters = 0;
for (final Tile tile : tiles) {
area += (tile.getClusterCount() / tile.getClusterDensity());
clusters += tile.getClusterCount();
}
return clusters/area;
}
}
}